scholarly journals Computational Analysis of a Prebiotic Amino Acid Synthesis with Reference to Extant Codon–Amino Acid Relationships

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1343
Author(s):  
Tolga Yaman ◽  
Jeremy N. Harvey
Keyword(s):  
Amino Acid ◽  
Density Functional ◽  
Computational Analysis ◽  
Density Functional Theory Calculations ◽  
Acid Synthesis ◽  
Keto Acid ◽  
Amino Acid Synthesis ◽  
Functional Theory ◽  
Energy Profiles ◽  
Keto Acids

Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.

scholarly journals Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

2021 ◽  
Vol 22 (6) ◽  
pp. 3244
Author(s):  
Charuvaka Muvva ◽  
Natarajan Arul Murugan ◽  
Venkatesan Subramanian
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Amyloid Β ◽  
Density Functional Theory Calculations ◽  
Tau Proteins ◽  
Functional Theory ◽  
Energy Profiles ◽  
Α Helix ◽  
Semi Empirical ◽  
Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

scholarly journals Surface and shape modification of mackinawite (FeS) nanocrystals by cysteine adsorption: a first-principles DFT-D2 study

2016 ◽  
Vol 18 (47) ◽  
pp. 32007-32020 ◽  
Author(s):  
N. Y. Dzade ◽  
A. Roldan ◽  
N. H. de Leeuw
Keyword(s):  
Density Functional Theory ◽  
Amino Acid ◽  
First Principles ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Dispersion Interactions ◽  
Shape Modification ◽  
Functional Theory ◽  
Shape Modulation

The surface and shape modulation of mackinawite (FeS) nanoparticles by amino acid cysteine adsorption is investigated using a first-principles density functional theory calculations, corrected for dispersion-interactions (DFT-D2).

scholarly journals Formation of Potassium 2-Hydroxy-6-naphthoate by Kolbe-Schmitt Carboxylation: A Joint Experimental and Theoretical Study

2019 ◽  
Author(s):  
So-Jin Ahn ◽  
Du-Hyeon Kim ◽  
Eung-Gun Kim ◽  
Yong-Kul Lee
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Reaction Pathway ◽  
Density Functional Theory Calculations ◽  
Spectroscopic Studies ◽  
Reaction Intermediates ◽  
Functional Theory ◽  
Complex Rearrangement ◽  
Energy Profiles ◽  
Naphthoic Acid

The reaction mechanism of the carboxylation of K-2-naphthoxide was investigated by density functional theory calculations and spectroscopic studies. The reaction intermediates and products were confirmed by CO2 adsorbed-FTIR and 1H-NMR measurements. Four steps of the reaction pathway were identified: CO2 activation, electrophilic substitution, CO2-K complex rearrangement, and H-shift, producing 2-hydroxy-1-naphthoic acid (2,1-HNA), 2-hydroxy-3-naphthoic acid (2,3-HNA), and 2-hydroxy-6-naphthoic acid (2,6-HNA). The occurrence of CO2-K complex rearrangement was also confirmed. These energy profiles of reaction pathways for the reaction intermediates were well consistent the experimental results on the carboxylation of K-2-naphthoxide.

scholarly journals Density Functional Theory Studies on the Synthesis of Poly(α-Amino Acid)s Via the Amine-Mediated Ring Opening Polymerizations of N-Carboxyanhydrides and N-Thiocarboxyanhydrides

2021 ◽  
Vol 9 ◽  
Author(s):  
Tianwen Bai ◽  
Botuo Zheng ◽  
Jun Ling
Keyword(s):  
Density Functional Theory ◽  
Amino Acid ◽  
Ring Opening ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
The Past

To synthesize well-defined poly (α-amino acid)s (PAAs), ring opening polymerizations (ROP) of cyclic monomers of α-amino acid N-carboxyanhydrides (NCAs) and N-thiocarboxyanhydrides (NTAs) are most widely used. In this mini-review, we summarize the mechanism details of the monomer preparation and ROP. The present study used density functional theory calculations to reveal the mechanisms together with experimental phenomena in the past decades. Detailed discussion includes normal amine mechanism and the selectivity of the initiators bearing various nucleophilic groups.

On the Linear Geometry of Lanthanide Hydroxide (Ln—OH, Ln=La-Lu)

2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Triple Bond ◽  
Density Functional ◽  
Valence Electron ◽  
Density Functional Theory Calculations ◽  
Electron Configuration ◽  
Functional Theory ◽  
Key Species ◽  
Pi Orbitals ◽  
Lanthanide Hydroxide ◽  
Linear Geometry

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.

On the Linear Geometry of Lanthanide Hydroxide (Ln—OH, Ln=La-Lu)

2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Triple Bond ◽  
Density Functional ◽  
Valence Electron ◽  
Density Functional Theory Calculations ◽  
Electron Configuration ◽  
Functional Theory ◽  
Key Species ◽  
Pi Orbitals ◽  
Lanthanide Hydroxide ◽  
Linear Geometry

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.

A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides

2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Cd Spectra ◽  
Functional Theory ◽  
Polyproline Ii ◽  
Solvent Dependence ◽  
Explicit Consideration ◽  
New Interpretation ◽  
Implicit And Explicit ◽  
Explicit Water

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.

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